algorithm

Total sequences

900
HIV subtyping: COMET
HIV subtype Number of sequences Percentage
PRRT and Integrase
16_A2D 3 0%
A1 213 34%
B 2 0%
C 71 11%
CRF11_cpx 3 0%
CRF25_cpx 3 0%
CRF45_cpx 1 0%
D 109 17%
G 61 10%
Undetermined 168 26%
PRRT only
16_A2D 2 4%
A1 24 42%
B 1 2%
C 5 9%
D 12 21%
G 4 7%
J 1 2%
Undetermined 8 14%
Integrase only
A1 62 30%
A2 1 0%
B 1 0%
C 26 12%
CRF02_AG 2 1%
D 73 35%
G 26 12%
Undetermined 18 9%
PMID:25120265*
HIV subtyping: REGA
HIV subtype Number of sequences Percentage
PRRT and Integrase
A1 293 46%
C 79 12%
D 103 16%
G 101 16%
J 58 9%
PRRT only
A1 28 49%
C 4 7%
D 11 19%
G 6 11%
H 1 2%
J 5 9%
K 2 4%
Integrase only
A1 65 31%
B 2 1%
C 28 13%
D 44 21%
G 26 12%
J 44 21%

Source: PMID: 23660484

HIV subtyping: Stanford hivdb
HIV subtype Number of sequences Percentage
PRRT and Integrase
A1 213 34%
A2 5 1%
A3 2 0%
A6 1 0%
A7 3 0%
B 14 2%
C 91 14%
CRF02_AG 6 1%
CRF06_cpx 2 0%
CRF09_cpx 41 6%
CRF11_cpx 2 0%
CRF25_cpx 2 0%
CRF45_cpx 18 3%
D 156 25%
G 75 12%
J 2 0%
Unknown 1 0%
PRRT only
A1 18 32%
A2 3 5%
A6 3 5%
A7 1 2%
B 4 7%
C 5 9%
CRF11_cpx 1 2%
CRF45_cpx 1 2%
D 10 18%
G 9 16%
Unknown 2 4%
Integrase only
A1 54 26%
A2 1 0%
A3 1 0%
B 11 5%
C 29 14%
CRF01_AE 2 1%
CRF02_AG 16 8%
CRF06_cpx 1 0%
CRF09_cpx 6 3%
D 69 33%
F 1 0%
G 16 8%
Unknown 2 1%

Source: hivdb.stanford.edu/page/hiv-subtyper.

HIV subtyping: Nearest neightbor (phylogenetics)
HIV subtype Number of sequences Percentage
PRRT and Integrase
02_AG 71 46%
11_cpx 3 2%
13_cpx 1 1%
21_A2D 1 1%
84_A1D 1 1%
A2 5 3%
D 71 46%
PRRT only
02_AG 9 64%
11_cpx 1 7%
A2 2 14%
B 1 7%
D 1 7%
Integrase only
02_AG 13 54%
112_01B 1 4%
25_cpx 1 4%
D 9 38%